This study investigates bacterial community transitions along the 2000 km salinity gradient of the Baltic Sea, one of the world's largest brackish water environments. Using 454 pyrosequencing of partial 16S rRNA genes, researchers analyzed 213 samples from 60 stations, revealing significant changes in bacterial community composition at both broad and fine phylogenetic levels. The brackish water community included a mix of freshwater and marine groups, along with unique populations. The Baltic Sea's long water residence time (3–30 years) suggests that the observed community is autochthonous, not a mix of fresh and saltwater. Unlike multicellular organisms, bacterial diversity in brackish conditions did not decline, possibly due to rapid bacterial adaptation filling ecological niches. The study identified distinct bacterial communities in freshwater-brackish, brackish, and brackish-marine zones, with SAR11 and Verrucomicrobia being prominent. The brackish community showed a shift towards Verrucomicrobia at salinities 5–10. Bacterial α-diversity did not show significant differences across salinity groups, suggesting that the community is maintained by adapted bacteria from marine and freshwater environments. The study highlights the importance of understanding brackish water microbiomes for functional and genomic investigations. The results indicate that bacteria have adapted more rapidly to brackish conditions than multicellular organisms, possibly due to their shorter generation times and dynamic genomes. This research provides a detailed taxonomic study of the Baltic Sea's brackish microbiome, offering insights into the ecological roles of its dominant bacterial groups.This study investigates bacterial community transitions along the 2000 km salinity gradient of the Baltic Sea, one of the world's largest brackish water environments. Using 454 pyrosequencing of partial 16S rRNA genes, researchers analyzed 213 samples from 60 stations, revealing significant changes in bacterial community composition at both broad and fine phylogenetic levels. The brackish water community included a mix of freshwater and marine groups, along with unique populations. The Baltic Sea's long water residence time (3–30 years) suggests that the observed community is autochthonous, not a mix of fresh and saltwater. Unlike multicellular organisms, bacterial diversity in brackish conditions did not decline, possibly due to rapid bacterial adaptation filling ecological niches. The study identified distinct bacterial communities in freshwater-brackish, brackish, and brackish-marine zones, with SAR11 and Verrucomicrobia being prominent. The brackish community showed a shift towards Verrucomicrobia at salinities 5–10. Bacterial α-diversity did not show significant differences across salinity groups, suggesting that the community is maintained by adapted bacteria from marine and freshwater environments. The study highlights the importance of understanding brackish water microbiomes for functional and genomic investigations. The results indicate that bacteria have adapted more rapidly to brackish conditions than multicellular organisms, possibly due to their shorter generation times and dynamic genomes. This research provides a detailed taxonomic study of the Baltic Sea's brackish microbiome, offering insights into the ecological roles of its dominant bacterial groups.